Thats why the cap is set at 125%, to allow for minor adjustment and inequities. If PB value was perfectly accurate, the cap might be set at 120%(plus we wouldn't need to play the games, just give it to the guy with the highest PB value).

I've done some statistical analysis and found that over a large sample of hitters, PB value was less than 2.5% off of what it should be; while for pitchers the number was less than 5%(part time starters and lower inning pitchers get the shaft, accounting for most of this inequity).

Thus when looking at Bonds compared to Arod, slight variation in each score(.3 PB) alters their positioning.